Index

A

a_cluster (uchrom.strc.comp.axes_pc.CompartmentCallerParams attribute) (uchrom.strc.comp.CompartmentCallerParams attribute) add() (chromdata.intervals.IntervalStore method) (chromdata.zarrcd.SpotPartitionWriter method) (uchrom_browser.DatasetStore method) add_annotation_features() (in module uchrom.fea) (in module uchrom.fea.annotation) add_peak_features() (in module uchrom.fea) (in module uchrom.fea.peaks) add_reference() (chromdata.ChromData method) add_sequence_features() (in module uchrom.fea) (in module uchrom.fea.sequence) add_structural_features() (in module uchrom.strc.enrichment) add_user_annotation() (chromdata.ChromData method) aggregate_over_tads() (in module uchrom.recon.fish._hic) aggregate_track_by_interval() (in module uchrom.fea) (in module uchrom.fea.peaks) aggregate_tracks() (in module uchrom.emb.cells) aggregate_tracks_by_interval() (in module uchrom.fea) (in module uchrom.fea.peaks)

align_embedding() (in module uchrom.emb.higashi) align_spots() (in module uchrom.im.trace) align_substructure_to_scaffold() (in module uchrom.recon.bulk.mds.transforms) allow_reflection (uchrom.recon.fish._assembly.AssemblyParams attribute) alpha (uchrom.recon.fish._assembly.AssemblyParams attribute) angle_weight (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) append_feature_registry_entry() (in module uchrom.fea) (in module uchrom.fea.registry) apply_distance_decay_prior() (in module uchrom.recon.bulk.mds) apply_transform() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.transforms) array() (chromdata.zarrcd.Container method) assemble() (in module uchrom.recon.fish._assembly) AssemblyParams (class in uchrom.recon.fish._assembly) axis_variance_cube() (in module uchrom.fea) (in module uchrom.fea.arc) axis_weight() (in module uchrom.fea) (in module uchrom.fea.arc)

B

backed (chromdata.backed.BackedChromData property) (chromdata.ChromData property) BackedArray (class in chromdata.backed) BackedChromData (class in chromdata.backed) BackedFrame (class in chromdata.backed) begin() (chromdata.zarrcd.SpotPartitionWriter method) bin_tracks (chromdata.ChromData property)

bins (chromdata.ChromData property) bins_from_loci() (in module chromdata.bins) bond_length (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) bond_log_probability() (in module uchrom.im.trace._polymer) bond_weight (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) BrowserError (class in uchrom_browser)

C

calc_directionality_index() (in module uchrom.strc.tad) (in module uchrom.strc.tad.di) call() (uchrom_browser.Workspace method) call_compartments() (in module uchrom.tl) call_compartments_axes_pc() (in module uchrom.strc.comp) (in module uchrom.strc.comp.axes_pc) call_compartments_multi() (in module uchrom.strc.enrichment) call_domains_fishnet() (in module uchrom.strc.tad) (in module uchrom.strc.tad.fishnet) call_domains_fishnet_trace() (in module uchrom.strc.tad) (in module uchrom.strc.tad.fishnet) call_loops() (in module uchrom.tl) call_loops_axiswise_f() (in module uchrom.strc.loop) (in module uchrom.strc.loop.axiswise_f) call_loops_multi() (in module uchrom.strc.enrichment) call_macs_bdgpeaks_from_bedgraph() (in module uchrom.fea) (in module uchrom.fea.peaks) call_macs_bdgpeaks_from_signal() (in module uchrom.fea) (in module uchrom.fea.peaks) call_macs_peaks_from_signal() (in module uchrom.fea) (in module uchrom.fea.peaks) call_peaks_from_signal() (in module uchrom.fea) (in module uchrom.fea.peaks) call_peaks_from_track() (in module uchrom.fea) (in module uchrom.fea.peaks) call_structures_multi() (in module uchrom.strc.enrichment) call_tads() (in module uchrom.tl) call_tads_by_pval() (in module uchrom.strc.tad) (in module uchrom.strc.tad.arc_pval) call_tads_di() (in module uchrom.strc.tad) (in module uchrom.strc.tad.di_caller) call_tads_multi() (in module uchrom.strc.enrichment) capture() (uchrom_browser.Workspace method) cauchy_combination() (in module uchrom.utils) (in module uchrom.utils.stats) cell_positions() (chromdata.ChromData method) cell_shapes_geodataframe() (chromdata.ChromData method) center_coords() (in module uchrom.recon.bulk.mds.transforms) centre_gap_factor (uchrom.recon.fish._assembly.AssemblyParams attribute) chromdata module chromdata (chromdata.UChromProject attribute) ChromData (class in chromdata) chromdata.backed module chromdata.bins module chromdata.intervals module

chromdata.results module chromdata.zarrcd module chromdata_path (chromdata.UChromProject attribute) chroms (chromdata.ChromData property) clear_cache() (chromdata.zarrcd.SpotRows method) close() (chromdata.backed.BackedChromData method) (chromdata.zarrcd.Container method) cluster_cells() (in module uchrom.emb.cells) cmds_init() (in module uchrom.recon.bulk.mds.torch_mds) coerce() (chromdata.intervals.IntervalStore class method) (chromdata.results.ResultsStore class method) columns (chromdata.backed.BackedFrame property) columns() (chromdata.zarrcd.SpotRows method) CompartmentCallerParams (class in uchrom.strc.comp) (class in uchrom.strc.comp.axes_pc) compute_annotation_features() (in module uchrom.fea) (in module uchrom.fea.annotation) compute_distances() (chromdata.backed.BackedChromData method) (chromdata.ChromData method) compute_peak_features() (in module uchrom.fea) (in module uchrom.fea.peaks) compute_radius_of_gyration() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.transforms) compute_sequence_features() (in module uchrom.fea) (in module uchrom.fea.sequence) compute_stress() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.torch_mds) compute_structural_features() (in module uchrom.strc.enrichment) connect() (in module uchrom_browser) contact_frequency() (in module uchrom.fea) (in module uchrom.fea.distance) contact_to_distance() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.fish._hic) Container (class in chromdata.zarrcd) container_kind() (in module chromdata.zarrcd) convergence_abs (uchrom.recon.fish._assembly.AssemblyParams attribute) convert() (in module uchrom.io.upgrade) coord_status() (chromdata.ChromData method) coords (chromdata.backed.BackedChromData property) coords_of() (chromdata.zarrcd.SpotRows method) copy() (chromdata.backed.BackedChromData method) (chromdata.ChromData method) create_app() (in module uchrom_browser) created_utc (chromdata.results.ResultRecord attribute) cut_lo (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) cut_up (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute)

D

dataset() (uchrom_browser.Workspace method) dataset_references (chromdata.ChromData property) DatasetStore (class in uchrom_browser) decode() (chromdata.zarrcd.SpotRows method) DEFAULT_CACHE_BYTES (in module chromdata.zarrcd) default_float_dtype() (in module uchrom.utils.stats) DEFAULT_ROW_GROUP_ROWS (in module chromdata.zarrcd) default_sigma_nm (uchrom.im.trace.SpotAlignerParams attribute) default_target() (in module uchrom.io.upgrade) DEFAULT_ZSTD_LEVEL (in module chromdata.zarrcd) describe() (chromdata.UChromProject method) (uchrom_browser.Workspace method) describe_links() (chromdata.ChromData method) detect_sisters (uchrom.im.trace.SpotAlignerParams attribute) detect_tad_boundaries() (in module uchrom.strc.tad) (in module uchrom.strc.tad.di)

device (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) (uchrom.recon.fish.GEMFISHParams attribute) DICallerParams (class in uchrom.strc.tad) (class in uchrom.strc.tad.di_caller) distance (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) distance_map() (in module uchrom.fea) (in module uchrom.fea.distance) DistanceMap (class in uchrom.fea) (class in uchrom.fea.distance) downsample_coords() (in module uchrom.recon.bulk.mds.transforms) dtype (chromdata.backed.BackedArray attribute) dtypes (chromdata.backed.BackedFrame property)

E

embed_cells() (in module uchrom.emb.cells) embedded_links() (chromdata.ChromData method) EMBER_PROTOCOL (in module uchrom.recon.sc.ember) empty (chromdata.backed.BackedFrame property) empty() (chromdata.zarrcd.SpotRows method) empty_bins() (in module chromdata.bins) encoding (chromdata.zarrcd.SpotRows attribute) end() (chromdata.zarrcd.SpotPartitionWriter method)

endpoint_k (uchrom.recon.fish._assembly.AssemblyParams attribute) engine_info() (in module uchrom.recon.sc.nucdyn) exclude_radius (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) exclude_weight (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) exists() (chromdata.zarrcd.Container method) expected_distance() (in module uchrom.im.trace._polymer) expected_distance_sq() (in module uchrom.im.trace._polymer)

F

fdr_cutoff (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) file_format_version() (in module uchrom.io.upgrade) file_sha256() (in module uchrom.fea.registry) files (chromdata.zarrcd.SpotRows attribute) fill_missing_distances() (in module uchrom.recon.bulk.mds) filter_normalize() (in module uchrom.fea) (in module uchrom.fea.arc) fish_distance_loss() (in module uchrom.recon.fish._losses) FISHnetParams (class in uchrom.strc.tad) (class in uchrom.strc.tad.fishnet) fit_scale_factor() (in module uchrom.im.trace._polymer) fit_scale_factor_from_matrix() (in module uchrom.im.trace._polymer)

format_version (chromdata.backed.BackedChromData property) frac (uchrom.strc.comp.axes_pc.CompartmentCallerParams attribute) (uchrom.strc.comp.CompartmentCallerParams attribute) (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) from_chromdata() (chromdata.UChromProject class method) from_dataframe() (chromdata.ChromData class method) from_fofct() (chromdata.ChromData class method) from_frame() (chromdata.intervals.IntervalTable class method) from_pyhim_trace() (chromdata.ChromData class method) from_seqfish_multiomics() (chromdata.ChromData class method) from_seqfish_multiomics_linked() (chromdata.ChromData class method) from_takei2025_cerebellum() (chromdata.ChromData class method) function (chromdata.results.ResultRecord attribute)

G

gap (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) gap_distance_from_contacts() (in module uchrom.recon.fish._assembly) gap_penalty (uchrom.im.trace.SpotAlignerParams attribute) GEMFISHParams (class in uchrom.recon.fish) get() (uchrom_browser.DatasetStore method) get_cell() (chromdata.backed.BackedChromData method) (chromdata.ChromData method) get_cells() (chromdata.ChromData method) get_chrom() (chromdata.backed.BackedChromData method) (chromdata.ChromData method)

get_device() (in module uchrom.recon.bulk.mds.torch_mds) (in module uchrom.strc.tad.di) (in module uchrom.utils) (in module uchrom.utils.stats) get_domains() (in module uchrom.strc.tad) (in module uchrom.strc.tad.di) get_dtype() (in module uchrom.recon.bulk.mds.torch_mds) (in module uchrom.strc.tad.di) get_trace() (chromdata.backed.BackedChromData method) (chromdata.ChromData method) group_attrs() (chromdata.zarrcd.Container method)

H

has_coords_table (chromdata.backed.BackedChromData property) head() (chromdata.backed.BackedFrame method) hic_alpha (uchrom.recon.fish.GEMFISHParams attribute) hic_fallback_beta (uchrom.recon.fish.GEMFISHParams attribute)

hic_fallback_c (uchrom.recon.fish.GEMFISHParams attribute) hic_kl_loss() (in module uchrom.recon.fish._losses) hierarchical (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute)

I

iloc (chromdata.backed.BackedFrame property) impute (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) impute() (in module uchrom.pp) index (chromdata.backed.BackedFrame property) index() (chromdata.zarrcd.SpotPartitionWriter method) infer_interval_kind() (in module chromdata.intervals) infer_kind() (in module chromdata.results) init_from_mds (uchrom.recon.fish._tad_level.Stage1Params attribute) init_scale (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) inner_cut (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute)

inner_max_iter (uchrom.recon.fish._assembly.AssemblyParams attribute) inputs (chromdata.results.ResultRecord attribute) inter_mds() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.inter) intervals (chromdata.ChromData property) IntervalStore (class in chromdata.intervals) IntervalTable (class in chromdata.intervals) is_coords (chromdata.zarrcd.SpotRows attribute) iter_cells() (chromdata.backed.BackedChromData method) (chromdata.ChromData method) iter_traces() (chromdata.backed.BackedChromData method) (chromdata.ChromData method) iterative (uchrom.recon.fish._assembly.AssemblyParams attribute)

K

k_sigma (uchrom.strc.comp.axes_pc.CompartmentCallerParams attribute) (uchrom.strc.comp.CompartmentCallerParams attribute) (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute)

kind (chromdata.intervals.IntervalTable property) (chromdata.results.ResultRecord attribute)

L

lambda_E (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) lambda_E_intra (uchrom.recon.fish.GEMFISHParams attribute) lambda_E_tad (uchrom.recon.fish.GEMFISHParams attribute) lambda_F (uchrom.recon.fish._tad_level.Stage1Params attribute) (uchrom.recon.fish.GEMFISHParams attribute) lambda_R (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish.GEMFISHParams attribute) link_anndata() (chromdata.ChromData method) link_cool() (chromdata.ChromData method) link_mudata() (chromdata.ChromData method) (chromdata.UChromProject method) link_scool() (chromdata.ChromData method) (chromdata.UChromProject method) link_spatialdata() (chromdata.ChromData method) (chromdata.UChromProject method) linked_adata (chromdata.ChromData property) linked_cool_path() (chromdata.ChromData method) links (chromdata.UChromProject attribute)

list() (uchrom_browser.DatasetStore method) load() (uchrom_browser.DatasetStore method) load_contact_matrix() (in module uchrom.recon.fish._hic) load_contacts() (in module uchrom.recon.sc.nucdyn) load_linked_anndata() (chromdata.ChromData method) load_linked_mudata() (chromdata.ChromData method) load_linked_scool() (chromdata.ChromData method) load_linked_spatialdata() (chromdata.ChromData method) load_mudata() (chromdata.UChromProject method) load_scool() (chromdata.UChromProject method) load_spatialdata() (chromdata.UChromProject method) load_tad_from_bed() (in module uchrom.strc.tad) (in module uchrom.strc.tad.utils) loci_of() (in module chromdata.bins) LoopCallerParams (class in uchrom.strc.loop) (class in uchrom.strc.loop.axiswise_f) lowess_log_log() (in module uchrom.utils) (in module uchrom.utils.stats) lr (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute)

M

macs_bdgpeaks_to_narrowpeak() (in module uchrom.fea) (in module uchrom.fea.peaks) mahalanobis_cost() (in module uchrom.im.trace._polymer) main() (in module uchrom.io.upgrade) (in module uchrom.recon.sc.nucdyn) map_loci_to_bins() (in module chromdata.bins) marker_features() (in module uchrom.emb.cells) match_scales (uchrom.recon.fish._assembly.AssemblyParams attribute) max_bins_per_tad (uchrom.recon.fish._intra_tad.Stage2Params attribute) max_fibers_per_chrom (uchrom.im.trace.SpotAlignerParams attribute) max_levels (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) max_skip (uchrom.im.trace.SpotAlignerParams attribute) max_thresholds (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) mean_distance_matrix() (in module uchrom.fea) (in module uchrom.fea.distance) mean_edge_weight_cutoff (uchrom.im.trace.SpotAlignerParams attribute) merge_tables() (in module uchrom.convention) merge_tol (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) min_bins (uchrom.strc.comp.axes_pc.CompartmentCallerParams attribute) (uchrom.strc.comp.CompartmentCallerParams attribute) min_cluster_size (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) min_coverage (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) min_size_frac (uchrom.strc.tad.di_caller.DICallerParams attribute) (uchrom.strc.tad.DICallerParams attribute) min_spots_per_fiber (uchrom.im.trace.SpotAlignerParams attribute) module chromdata chromdata.backed chromdata.bins chromdata.intervals chromdata.results chromdata.zarrcd uchrom.convention uchrom.emb.cells uchrom.emb.hic uchrom.emb.higashi uchrom.fea uchrom.fea.annotation uchrom.fea.arc uchrom.fea.distance uchrom.fea.peaks uchrom.fea.project uchrom.fea.registry uchrom.fea.sequence uchrom.im uchrom.im.trace uchrom.im.trace._polymer uchrom.io uchrom.io.upgrade uchrom.pl uchrom.pl.structure_3d uchrom.pl.trace_stats uchrom.pp uchrom.recon.bulk.mds uchrom.recon.bulk.mds.inter uchrom.recon.bulk.mds.torch_mds uchrom.recon.bulk.mds.transforms uchrom.recon.fish uchrom.recon.fish._assembly uchrom.recon.fish._hic uchrom.recon.fish._intra_tad uchrom.recon.fish._losses uchrom.recon.fish._tad_level uchrom.recon.sc.ember uchrom.recon.sc.nucdyn uchrom.strc.comp uchrom.strc.enrichment uchrom.strc.loop uchrom.strc.tad uchrom.strc.tad.di uchrom.strc.tad.utils uchrom.tl uchrom.utils uchrom.utils.stats

N

n_bins (chromdata.ChromData property) n_cells (chromdata.backed.BackedChromData property) (chromdata.ChromData property) n_clusters (uchrom.strc.comp.axes_pc.CompartmentCallerParams attribute) (uchrom.strc.comp.CompartmentCallerParams attribute) n_ensemble (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) n_iter (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) n_louvain_runs (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute)

n_partitions (chromdata.zarrcd.SpotRows property) n_spots (chromdata.backed.BackedChromData property) (chromdata.ChromData property) n_traces (chromdata.backed.BackedChromData property) (chromdata.ChromData property) native_available() (in module uchrom.recon.sc.nucdyn) ndim (chromdata.backed.BackedArray attribute) normalise_bins() (in module chromdata.bins) normalize_counts() (in module uchrom.emb.cells) normalize_distances() (in module uchrom.recon.bulk.mds)

O

optimiser (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute)

outer_cut (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) outer_max_iter (uchrom.recon.fish._assembly.AssemblyParams attribute)

P

pages() (uchrom_browser.Workspace method) params (chromdata.results.ResultRecord attribute) parquet() (chromdata.zarrcd.Container method) parse_legacy_call() (in module uchrom.convention) part_chrom (chromdata.zarrcd.SpotPartitionWriter attribute) partition_dirs() (in module chromdata.zarrcd) partition_range() (chromdata.zarrcd.SpotRows method) partitioned (chromdata.backed.BackedChromData property) partitioned_mds() (in module uchrom.recon.bulk.mds) partitions (chromdata.zarrcd.SpotPartitionWriter attribute) persistence_length_bp (uchrom.im.trace.SpotAlignerParams attribute) PERSISTENCE_LENGTH_BP_DEFAULT (in module uchrom.im.trace._polymer) pf() (chromdata.zarrcd.SpotRows method) physical() (chromdata.zarrcd.SpotRows method) plain_columns (chromdata.zarrcd.SpotPartitionWriter attribute) plateau_size (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) plot_contact_map() (in module uchrom.pl) (in module uchrom.pl.trace_stats) plot_distance_matrix() (in module uchrom.pl) (in module uchrom.pl.trace_stats)

plot_rg_histogram() (in module uchrom.pl) (in module uchrom.pl.trace_stats) plot_structure_3d() (in module uchrom.pl) (in module uchrom.pl.structure_3d) polymer_energy() (in module uchrom.recon.fish._losses) prefetch() (chromdata.zarrcd.Container method) prefetch_frames() (chromdata.zarrcd.Container method) prefix (chromdata.zarrcd.SpotPartitionWriter attribute) procrustes_alignment() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.transforms) project_interval_features_to_bins() (in module uchrom.fea) (in module uchrom.fea.project) project_interval_features_to_spots() (in module uchrom.fea) (in module uchrom.fea.project) prominence (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) provenance (chromdata.results.ResultRecord property) pval_cutoff (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute)

R

radius_of_gyration() (in module uchrom.fea) (in module uchrom.fea.distance) random_state (uchrom.strc.comp.axes_pc.CompartmentCallerParams attribute) (uchrom.strc.comp.CompartmentCallerParams attribute) read() (chromdata.ChromData class method) read_all() (chromdata.zarrcd.SpotRows method) read_bedgraph() (in module uchrom.fea) (in module uchrom.fea.peaks) read_frame() (chromdata.zarrcd.Container method) read_gtf() (in module uchrom.fea) (in module uchrom.fea.annotation) read_ranges() (chromdata.zarrcd.SpotRows method) read_small_parts() (in module chromdata.zarrcd) rebuild_bins() (chromdata.backed.BackedChromData method) (chromdata.ChromData method) reconstruct_ember() (in module uchrom.recon.sc.ember) reconstruct_gem_fish() (in module uchrom.recon.fish) reconstruct_intra_tad() (in module uchrom.recon.fish._intra_tad) reconstruct_nucdyn() (in module uchrom.recon.sc.nucdyn)

reconstruct_sc() (in module uchrom.tl) reconstruct_tad_level() (in module uchrom.recon.fish._tad_level) record() (chromdata.results.ResultsStore method) records() (chromdata.results.ResultsStore method) reflect_threshold (uchrom.recon.fish._assembly.AssemblyParams attribute) rel_path() (chromdata.zarrcd.SpotPartitionWriter method) remove() (uchrom_browser.DatasetStore method) resolution (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) resolve_chroms() (in module uchrom.convention) resolve_link_path() (chromdata.ChromData method) ResultRecord (class in chromdata.results) results (chromdata.ChromData property) ResultsStore (class in chromdata.results) rg_loss() (in module uchrom.recon.fish._losses) rg_squared() (in module uchrom.recon.fish._losses) run() (in module uchrom.emb.higashi) run_mds() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.torch_mds)

S

scaling_exponent_fixed (uchrom.im.trace.SpotAlignerParams attribute) schicluster_features() (in module uchrom.emb.hic) schicluster_impute() (in module uchrom.emb.hic) scool_cell_features() (in module uchrom.emb.hic) select_spots() (in module uchrom.convention) selected_cells() (uchrom_browser.Workspace method) selection_inputs() (in module uchrom.convention) serve() (in module uchrom_browser) set() (chromdata.results.ResultsStore method) set_cell_positions() (chromdata.ChromData method) (chromdata.UChromProject method) set_cell_shapes() (chromdata.ChromData method) set_cell_spatial_coordinates() (chromdata.ChromData method) (chromdata.UChromProject method) shape (chromdata.backed.BackedArray property) (chromdata.backed.BackedFrame property) sister_pair_radius_nm (uchrom.im.trace.SpotAlignerParams attribute) size (chromdata.backed.BackedArray property) size_exclusion (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) smacof() (in module uchrom.recon.bulk.mds.torch_mds) smooth_with_moving_average() (in module uchrom.strc.tad.di) smoothing_param (uchrom.strc.tad.di_caller.DICallerParams attribute) (uchrom.strc.tad.DICallerParams attribute)

sort_order() (in module chromdata.zarrcd) source_result (chromdata.intervals.IntervalTable property) split_chrom (chromdata.zarrcd.SpotPartitionWriter attribute) split_spot_tracks() (in module chromdata.bins) spot_tracks (chromdata.backed.BackedChromData property) (chromdata.ChromData property) SpotAlignerParams (class in uchrom.im.trace) SpotPartitionWriter (class in chromdata.zarrcd) SpotRows (class in chromdata.zarrcd) spots (chromdata.backed.BackedChromData property) spots_with_loci() (chromdata.backed.BackedChromData method) (chromdata.ChromData method) stage1_ensemble (uchrom.recon.fish.GEMFISHParams attribute) stage1_iter (uchrom.recon.fish.GEMFISHParams attribute) stage1_lr (uchrom.recon.fish.GEMFISHParams attribute) stage1_optimiser (uchrom.recon.fish.GEMFISHParams attribute) Stage1Params (class in uchrom.recon.fish._tad_level) stage2_ensemble (uchrom.recon.fish.GEMFISHParams attribute) stage2_iter (uchrom.recon.fish.GEMFISHParams attribute) stage2_lr (uchrom.recon.fish.GEMFISHParams attribute) Stage2Params (class in uchrom.recon.fish._intra_tad) store_and_return() (in module uchrom.convention)

T

table_provenance() (in module uchrom.fea.registry) tad_di_min_size_frac (uchrom.recon.fish.GEMFISHParams attribute) tad_di_smoothing (uchrom.recon.fish.GEMFISHParams attribute) tad_di_window (uchrom.recon.fish.GEMFISHParams attribute) tad_max_size_frac (uchrom.recon.fish.GEMFISHParams attribute) tad_regions_to_bin_indices() (in module uchrom.strc.tad.utils) TADCallerParams (class in uchrom.strc.tad) (class in uchrom.strc.tad.arc_pval) take() (chromdata.zarrcd.SpotRows method) tau_nm_per_bp (uchrom.im.trace.SpotAlignerParams attribute) tfidf_lsi() (in module uchrom.emb.cells) threshold_max (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) threshold_min (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) threshold_step (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) thresholds (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute)

to_anndata() (chromdata.backed.BackedChromData method) (chromdata.ChromData method) to_bins() (chromdata.intervals.IntervalStore method) (chromdata.intervals.IntervalTable method) to_dataframe() (chromdata.backed.BackedChromData method) (chromdata.ChromData method) to_dict() (chromdata.results.ResultsStore method) to_fofct() (chromdata.ChromData method) to_frame() (chromdata.zarrcd.SpotRows method) to_memory() (chromdata.backed.BackedChromData method) (chromdata.ChromData method) to_numpy() (chromdata.backed.BackedArray method) to_pandas() (chromdata.backed.BackedFrame method) to_spatialdata() (chromdata.ChromData method) tools() (uchrom_browser.Workspace method) torch_mds() (in module uchrom.recon.bulk.mds.torch_mds) track_names() (chromdata.ChromData method) tracks (chromdata.ChromData property) tracks_spot_view() (chromdata.backed.BackedChromData method) (chromdata.ChromData method)

U

uchrom.convention module uchrom.emb.cells module uchrom.emb.hic module uchrom.emb.higashi module uchrom.fea module uchrom.fea.annotation module uchrom.fea.arc module uchrom.fea.distance module uchrom.fea.peaks module uchrom.fea.project module uchrom.fea.registry module uchrom.fea.sequence module uchrom.im module uchrom.im.trace module uchrom.im.trace._polymer module uchrom.io module uchrom.io.upgrade module uchrom.pl module uchrom.pl.structure_3d module uchrom.pl.trace_stats module uchrom.pp module uchrom.recon.bulk.mds module uchrom.recon.bulk.mds.inter module

uchrom.recon.bulk.mds.torch_mds module uchrom.recon.bulk.mds.transforms module uchrom.recon.fish module uchrom.recon.fish._assembly module uchrom.recon.fish._hic module uchrom.recon.fish._intra_tad module uchrom.recon.fish._losses module uchrom.recon.fish._tad_level module uchrom.recon.sc.ember module uchrom.recon.sc.nucdyn module uchrom.strc.comp module uchrom.strc.enrichment module uchrom.strc.loop module uchrom.strc.tad module uchrom.strc.tad.di module uchrom.strc.tad.utils module uchrom.tl module uchrom.utils module uchrom.utils.stats module uchrom_version (chromdata.results.ResultRecord attribute) UChromProject (class in chromdata) unique_spot_intervals() (in module uchrom.fea) (in module uchrom.fea.project) UNSET (in module uchrom.convention) upgrade_h5cd() (in module uchrom.io.upgrade) user_annotations (chromdata.ChromData property)

V

validate() (chromdata.UChromProject method) validate_intervals() (in module chromdata.intervals) validate_links() (chromdata.ChromData method) validate_value() (in module chromdata.results)

value (chromdata.results.ResultRecord attribute) verbose (uchrom.im.trace.SpotAlignerParams attribute) (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) (uchrom.recon.fish.GEMFISHParams attribute)

W

window (uchrom.strc.tad.di_caller.DICallerParams attribute) (uchrom.strc.tad.DICallerParams attribute) window_bp (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) window_size (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute)

Workspace (class in uchrom_browser) write() (chromdata.backed.BackedChromData method) (chromdata.ChromData method) write_empty() (chromdata.zarrcd.SpotPartitionWriter method) write_zarr() (in module chromdata.zarrcd) writer() (chromdata.ChromData class method)

Z

ZARR_LAYOUT_VERSION (in module chromdata.zarrcd)

ZARR_LAYOUTS (in module chromdata.zarrcd)